Crystal structure and Hirshfeld surface analysis of dimethyl 2-oxo-4-(pyridin-2-yl)-6-(thio­phen-2-yl)cyclo­hex-3-ene-1,3-di­carboxyl­ate

Naghiyev, F.N.; Khrustalev, V.N.; Akkurt, M.; Huseynov, E.Z.; Bhattarai, A.; Khalilov, A.N.; Mamedov, İ.G.

doi:10.1107/S2056989024004687

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Volume 80| Part 6| June 2024| Pages 654-658

https://doi.org/10.1107/S2056989024004687

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Crystal structure and Hirshfeld surface analysis of dimethyl 2-oxo-4-(pyridin-2-yl)-6-(thiophen-2-yl)cyclohex-3-ene-1,3-dicarboxylate

Farid N. Naghiyev,^a Victor N. Khrustalev,^b,^c Mehmet Akkurt,^d ^* Elnur Z. Huseynov,^a Ajaya Bhattarai,^e ^* Ali N. Khalilov ^f,^a and İbrahim G. Mamedov ^a

^aDepartment of Chemistry, Baku State University, Z. Khalilov str. 23, Az, 1148, Baku, Azerbaijan, ^bPeoples' Friendship University of Russia (RUDN University), Miklukho-Maklay St.6, Moscow, 117198, Russian Federation, ^cN. D. Zelinsky Institute of Organic Chemistry RAS, Leninsky Prosp. 47, Moscow, 119991, Russian Federation, ^dDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Türkiye, ^eDepartment of Chemistry, M.M.A.M.C (Tribhuvan University) Biratnagar, Nepal, and ^f"Composite Materials" Scientific Research Center, Azerbaijan State Economic University (UNEC), Murtuza Mukhtarov str. 194, Az 1065, Baku, Azerbaijan
^*Correspondence e-mail: akkurt@erciyes.edu.tr, ajaya.bhattarai@mmamc.tu.edu.np

Edited by S.-L. Zheng, Harvard University, USA (Received 24 April 2024; accepted 20 May 2024; online 24 May 2024)

In the title compound, C₁₉H₁₇NO₅S, the cyclohexene ring adopts nearly an envelope conformation. In the crystal, molecules are linked by C—H⋯O hydrogen bonds, forming a three-dimensional network. In addition, C—H⋯π interactions connect the molecules by forming layers parallel to the (010) plane. According to the Hirshfeld surface analysis, H⋯H (36.9%), O⋯H/H⋯O (31.0%), C⋯H/H⋯C (18.9%) and S⋯H/H⋯S (7.9%) interactions are the most significant contributors to the crystal packing.

Keywords: crystal structure; thiophene ring; pyridine ring; cyclohexene ring; Hirshfeld surface analysis.

CCDC reference: 2356669

1. Chemical context

The class of molecules known as carbo- and heterocycles, arguably the most important, has a significant impact on the synthesis of various functionalized systems that have found diverse research and commercial applications (Huseynov et al., 2023 ; Akkurt et al., 2023 ). Bioactive natural and synthetic compounds frequently incorporate carbocycles and heterocycles as fundamental structural components. Moreover, these compounds may play an important role in organic synthesis as starting materials (Maharramov et al., 2022 ; Khalilov et al., 2023a ,b ). These derivatives have found broad applications in coordination chemistry (Gurbanov et al., 2021 ; Mahmoudi et al., 2021 ), medicinal chemistry (Askerova, 2022 ) and materials chemistry (Velásquez et al., 2019 ; Afkhami et al., 2019 ). These ring systems are utilized in various applications, spanning pharmaceuticals, ligands, catalysts, materials and beyond (Maharramov et al., 2021 , Sobhi & Faisal, 2023 ). Functionalized systems incorporating cyclohexanone, pyridine and thiophene motifs have demonstrated diverse biological activities, including molluscicidal, anticancer, antioxidant, cytotoxic, anti-inflammatory, herbicidal, pesticidal, antibacterial, and more (Erenler et al., 2022 ; Atalay et al., 2022 ; Donmez & Turkyılmaz, 2022 ). The broad application of these systems has garnered significant attention toward the efficient and regioselective development of such compounds. In summary, the synthesized compound offers a unique combination of structural features, including heteroatom diversity, conjugation, strategic functional group placement, and potential biological relevance. Analysis of its structure and properties can provide valuable contributions to the broader field of carbo- and heterocyclic chemistry and may have implications for various applications, including materials science and medicinal chemistry. Hence, within the context of structural studies (Abdinov et al., 2004 , 2012 , 2014 ; Naghiyev et al., 2020 , 2021a , 2022 ), we present the crystal structure and Hirshfeld surface analysis of the title compound, dimethyl 2-oxo-4-(pyridin-2-yl)-6-(thiophen-2-yl)cyclohex-3-ene-1,3-dicarboxylate.

2. Structural commentary

In the title compound (Fig. 1), the cyclohexene ring (C1–C6) adopts nearly an envelope conformation [puckering parameters (Cremer & Pople, 1975 ) are Q_T = 0.526 (2) Å, θ = 53.9 (2)° and φ = 117.3 (3)°]. The cyclohexene ring (r.m.s deviation = 0.002 Å) makes dihedral angles of 84.46 (11) and 29.49 (10)° with the thiophene (S1/C9–C12) and pyridine (N1/C13–C17) rings, respectively. The angle between the thiophene and pyridine rings is 77.04 (11)°. The C8—O3—C7—C2, O2—C7—C2—C3, C19—O5—C18—C6 and O4—C18—C6—C5 torsion angles are −169.87 (18), −70.3 (2), 174.97 (15) and 107.7 (2)°, respectively. The geometric properties of the title compound are normal and consistent with those of the related compounds described in the Database survey (Section 4).

Figure 1
The molecular structure of the title compound, showing the atom labelling and displacement ellipsoids drawn at the 50% probability level.

3. Supramolecular features and Hirshfeld surface analysis

In the crystal, molecules are linked by C—H⋯O hydrogen bonds, forming a three-dimensional network (Table 1; Figs. 2 and 3). In addition, C—H⋯π interactions connect the molecules, forming layers parallel to the (010) plane, represented by the distances between the same Cg1 and the same Cg2 centroids (Table 1; Figs. 4 and 5). The lengths of the C—H⋯π interactions are similar to the proper hydrogen bonds in the crystal structures. This is reasonable for carbo- and heterocycles (Nishio, 2011 ).

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the S1/C9–C12 thiophene and N1/C13–C17 pyridine rings, respectively.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C3—H3⋯O3ⁱ	1.00	2.64	3.625 (2)	168
C8—H8C⋯O2ⁱⁱ	0.98	2.35	3.215 (3)	146
C11—H11⋯O1ⁱⁱⁱ	0.95	2.62	3.193 (2)	119
C12—H12⋯O4^iv	0.95	2.50	3.446 (2)	180
C14—H14⋯O2^v	0.95	2.61	3.468 (2)	151
C16—H16⋯O1^vi	0.95	2.52	3.305 (3)	140
C19—H19B⋯O2^vii	0.98	2.64	3.584 (3)	161
C4—H4A⋯Cg2ⁱⁱ	0.99	2.94	3.841 (2)	152
C19—H19C⋯Cg1^viii	0.98	2.78	3.659 (3)	149
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) ; (vi) ; (vii) ; (viii) .

Figure 2
View of partial packing along the b axis of the title compound with C—H⋯O hydrogen bonds shown as dashed lines.

Figure 3
View of partial packing along the a axis of the title compound with C—H⋯O hydrogen bonds shown as dashed lines.

Figure 4
A view of the packing along the a axis of the title compound with C—H⋯π interactions shown as dashed lines.

Figure 5
A view of the packing along the b axis of the title compound with C—H⋯π interactions shown as dashed lines.

Crystal Explorer 17.5 (Spackman et al., 2021 ) was used to generate Hirshfeld surfaces and two-dimensional fingerprint plots in order to quantify the intermolecular interactions in the crystal. The Hirshfeld surfaces were mapped over d_norm in the range −0.2536 (red) to +1.2159 (blue) a.u. (Fig. 6). The most important interatomic contact is H⋯H as it makes the highest contribution to the crystal packing (36.9%, Fig. 7b). Other major contributors are O⋯H/H⋯O (31.0%, Fig. 7c), C⋯H/H⋯C (18.9%, Fig. 7d) and S⋯H/H⋯S (7.9%, Fig. 7e) interactions. Other, smaller contributions are made by N⋯H/H⋯N (2.6%), O⋯O (1.1%), O⋯C/C⋯O (0.9%), N⋯C/C⋯N (0.4%) and C⋯C (0.2%) interactions. This distribution is typical for such cyclohexene compounds (Naghiyev et al., 2024 ).

Figure 6
(a) Front and (b) back sides of the three-dimensional Hirshfeld surface of the title compound mapped over d_norm.

Figure 7
The two-dimensional fingerprint plots, showing (a) all interactions, and delineated into (b) H⋯H, (c) O⋯H/H⋯O, (d) C⋯H/H⋯C and (e) S⋯H/H⋯S interactions [d_e and d_i represent the distances from a point on the Hirshfeld surface to the nearest atoms outside (external) and inside (internal) the surface, respectively].

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.43, last update November 2022; Groom et al., 2016 ) for a central cyclohexene or -hexane ring yielded nine compounds related to the title compound, viz. CSD refcodes WOMWUU [(I); Naghiyev et al., 2024], UPOMOE [(II); Naghiyev et al., 2021b ], ZOMDUD [(III); Gein et al., 2019 ], PEWJUZ [(IV); Fatahpour et al., 2018 ], OZUKAX [(V); Tkachenko et al., 2014 ], IFUDOD ((VI); Gein et al., 2007 ], IWEVOV [(VII); Mohan et al., 2003 ], IWEVUB [(VIII); Mohan et al., 2003] and HALROB [(IX); Ravikumar & Mehdi, 1993 ].

Comparing the title compound and previously published structures, the published structures (Fig. 8) appear to have much higher symmetry space groups. While the title compound crystallizes in the triclinic space group P1 with Z = 1, (I), (II) and (III) crystallize in the monoclinic space group P2₁/c, with Z = 4, (IV) in I2/c with Z = 4, (VI), (VIII) and (IX) in P2₁/n with Z = 4, and (V) and (VII) in the orthorhombic space group Pbca with Z = 8.

Figure 8
The nine other published cyclohexene/hexane-based structures.

5. Synthesis and crystallization

For a novel synthesis of the title compound, a solution of 1-(pyridin-2-yl)-3-(thiophen-2-yl)prop-2-en-1-one (7 mmol) and dimethyl-1,3-acetonedicarboxylate (5.2 mmol) in methanol (30 mL) was stirred for 10 min. Then N-methylpiperazine (3 drops) was added to the reaction mixture, which was stirred for 48 h at room temperature. Then 20 mL of methanol were removed from the reaction mixture, which was left overnight. The precipitated crystals were separated by filtration and recrystallized from an ethanol/water (1:1) solution (m.p. = 480 K, yield 69%).

¹H NMR (300 MHz, DMSO-d₆, ppm.): 3.30 (dd, 2H, CH₂, ²J_H–H = 16.3 and ³J_H–H = 8.3); 3.65 (s, 6H, 2OCH₃); 4.02 (dd, 1H, CH, ³J_H–H = 8.3, ³J_H–H = 13.3); 4.20 (d, 1H, CH, ³J_H–H = 13.3); 7.00 (t, 1H, CH_thien., ³J_H–H = 5.1); 7.09 (d, 1H, CH_thien., ³J_H–H = 3.5); 7.41 (d, 1H, CH_thien., ³J_H–H = 5.1); 7.46 (t, 1H, CH_pyrid., ³J_H–H = 7.4); 7.76 (d, 1H, CH_pyrid., ³J_H–H = 7.4); 7.91 (t, 1H, CH_pyrid., ³J_H–H = 5.7); 8.63 (d, 1H, CH_pyrid., ³J_H–H = 5.7). ¹³C NMR (75 MHz, DMSO-d₆, ppm.): 35.47 (CH₂), 38.23 (CH), 52.24 (OCH₃), 52.43 (OCH₃), 60.45 (CH), 123.58 (CH_pyrid.), 125.20 (CH_pyrid.), 125.61 (CH_pyrid.), 125.77 (CH_pyrid.), 127.47 (CH_thien.), 131.43 (C_quat.), 137.93 (CH_thien.), 144.28 (C_thien.), 149.49 (CH_thien.), 153.21 (C_quat.), 155.14 (C_quat.), 166.83 (CO), 169.52 (CO), 191.68 (C=O).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. All C-bound H atoms were placed in calculated positions (C—H = 0.95 −1.00 Å) and refined as riding with U_iso(H) = 1.2 or 1.5U_eq(C).

Table 2
Experimental details

Crystal data
Chemical formula	C₁₉H₁₇NO₅S
M_r	371.39
Crystal system, space group	Triclinic, P1
Temperature (K)	100
a, b, c (Å)	5.5260 (1), 8.5012 (1), 10.1076 (2)
α, β, γ (°)	110.910 (2), 98.128 (1), 96.006 (1)
V (Å³)	432.88 (1)
Z	1
Radiation type	Cu Kα
μ (mm⁻¹)	1.94
Crystal size (mm)	0.25 × 0.23 × 0.09

Data collection
Diffractometer	XtaLAB Synergy, Dualflex, HyPix
Absorption correction	Gaussian (CrysAlis PRO; Rigaku OD, 2022 $[Rigaku OD (2022). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )
T_min, T_max	0.647, 0.840
No. of measured, independent and observed [I > 2σ(I)] reflections	18199, 3530, 3524
R_int	0.023
(sin θ/λ)_max (Å⁻¹)	0.634

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.023, 0.059, 1.06
No. of reflections	3530
No. of parameters	238
No. of restraints	3
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.22, −0.18
Absolute structure	Flack x determined using 1675 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	0.003 (7)
Computer programs: CrysAlis PRO (Rigaku OD, 2022 $[Rigaku OD (2022). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ ), SHELXT2014/5 (Sheldrick, 2015a ), SHELXL2019/3 (Sheldrick, 2015b ), ORTEP-3 for Windows (Farrugia, 2012 ) and PLATON (Spek, 2020 ).

Supporting information

CCDC reference: 2356669

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989024004687/oi2007sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989024004687/oi2007Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989024004687/oi2007Isup3.cml

checkCIF report

Computing details top

Dimethyl 2-oxo-4-(pyridin-2-yl)-6-(thiophen-2-yl)cyclohex-3-ene-1,3-dicarboxylate top

Crystal data top

C₁₉H₁₇NO₅S	Z = 1
M_r = 371.39	F(000) = 194
Triclinic, P1	D_x = 1.425 Mg m⁻³
a = 5.5260 (1) Å	Cu Kα radiation, λ = 1.54184 Å
b = 8.5012 (1) Å	Cell parameters from 16321 reflections
c = 10.1076 (2) Å	θ = 4.8–77.4°
α = 110.910 (2)°	µ = 1.94 mm⁻¹
β = 98.128 (1)°	T = 100 K
γ = 96.006 (1)°	Prism, colourless
V = 432.88 (1) Å³	0.25 × 0.23 × 0.09 mm

Data collection top

XtaLAB Synergy, Dualflex, HyPix diffractometer	3524 reflections with I > 2σ(I)
Radiation source: micro-focus sealed X-ray tube	R_int = 0.023
φ and ω scans	θ_max = 77.8°, θ_min = 4.8°
Absorption correction: gaussian (CrysAlisPro; Rigaku OD, 2022)	h = −6→6
T_min = 0.647, T_max = 0.840	k = −10→10
18199 measured reflections	l = −12→12
3530 independent reflections

Refinement top

Refinement on F²	H-atom parameters constrained
Least-squares matrix: full	w = 1/[σ²(F_o²) + (0.0337P)² + 0.097P] where P = (F_o² + 2F_c²)/3
R[F² > 2σ(F²)] = 0.023	(Δ/σ)_max < 0.001
wR(F²) = 0.059	Δρ_max = 0.22 e Å⁻³
S = 1.06	Δρ_min = −0.17 e Å⁻³
3530 reflections	Extinction correction: SHELXL2019/2 (Sheldrick, 2015b), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
238 parameters	Extinction coefficient: 0.0131 (14)
3 restraints	Absolute structure: Flack x determined using 1675 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
Hydrogen site location: inferred from neighbouring sites	Absolute structure parameter: 0.003 (7)

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.6259 (4)	0.3716 (2)	0.6011 (2)	0.0132 (4)
C2	0.7320 (4)	0.3495 (2)	0.46536 (19)	0.0127 (4)
H2	0.898999	0.422837	0.493270	0.015*
C3	0.5592 (4)	0.4059 (2)	0.36259 (19)	0.0136 (4)
H3	0.390686	0.337398	0.343691	0.016*
C4	0.5382 (4)	0.5930 (2)	0.4416 (2)	0.0146 (4)
H4A	0.703452	0.664844	0.465810	0.017*
H4B	0.425908	0.630379	0.377470	0.017*
C5	0.4396 (3)	0.6170 (2)	0.5780 (2)	0.0134 (4)
C6	0.4809 (4)	0.5121 (2)	0.64983 (19)	0.0129 (4)
C7	0.7580 (4)	0.1653 (2)	0.3869 (2)	0.0142 (4)
C8	1.0028 (4)	−0.0161 (3)	0.2524 (3)	0.0281 (5)
H8A	0.894696	−0.044480	0.158603	0.042*
H8B	0.954145	−0.100288	0.293541	0.042*
H8C	1.175204	−0.017674	0.239795	0.042*
C9	0.6332 (4)	0.3713 (2)	0.2190 (2)	0.0144 (4)
C10	0.5052 (4)	0.2567 (3)	0.0887 (2)	0.0188 (4)
H10	0.352786	0.185818	0.077251	0.023*
C11	0.6230 (4)	0.2541 (3)	−0.0286 (2)	0.0211 (4)
H11	0.557058	0.181613	−0.126180	0.025*
C12	0.8386 (4)	0.3654 (3)	0.0135 (2)	0.0198 (4)
H12	0.941797	0.380424	−0.050162	0.024*
C13	0.2915 (4)	0.7557 (2)	0.6266 (2)	0.0138 (4)
C14	0.3097 (4)	0.8926 (2)	0.5803 (2)	0.0170 (4)
H14	0.419867	0.900060	0.517866	0.020*
C15	0.1640 (4)	1.0168 (2)	0.6273 (2)	0.0193 (4)
H15	0.173481	1.111309	0.597847	0.023*
C16	0.0042 (4)	1.0017 (3)	0.7177 (2)	0.0192 (4)
H16	−0.098664	1.084695	0.750789	0.023*
C17	−0.0018 (4)	0.8619 (3)	0.7589 (2)	0.0182 (4)
H17	−0.109760	0.852595	0.822018	0.022*
C18	0.3784 (4)	0.5217 (2)	0.7826 (2)	0.0132 (4)
C19	0.3964 (4)	0.6765 (3)	1.0269 (2)	0.0222 (4)
H19A	0.220812	0.685154	1.005687	0.033*
H19B	0.484406	0.781046	1.106272	0.033*
H19C	0.411825	0.578189	1.054703	0.033*
N1	0.1361 (3)	0.7402 (2)	0.71452 (18)	0.0161 (3)
O1	0.6615 (3)	0.27874 (17)	0.66693 (15)	0.0178 (3)
O2	0.5944 (3)	0.04488 (18)	0.35502 (15)	0.0196 (3)
O3	0.9794 (3)	0.15282 (18)	0.34916 (15)	0.0188 (3)
O4	0.2142 (3)	0.41766 (17)	0.78248 (15)	0.0175 (3)
O5	0.5031 (3)	0.65445 (18)	0.89989 (14)	0.0168 (3)
S1	0.90193 (7)	0.47674 (5)	0.19781 (5)	0.01854 (13)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0118 (9)	0.0139 (8)	0.0134 (8)	0.0017 (7)	0.0025 (7)	0.0047 (7)
C2	0.0131 (9)	0.0131 (8)	0.0128 (8)	0.0041 (7)	0.0039 (7)	0.0049 (7)
C3	0.0140 (9)	0.0149 (9)	0.0123 (8)	0.0022 (7)	0.0033 (7)	0.0056 (7)
C4	0.0166 (10)	0.0143 (8)	0.0152 (9)	0.0053 (7)	0.0044 (7)	0.0072 (7)
C5	0.0122 (9)	0.0125 (8)	0.0144 (8)	0.0016 (7)	0.0026 (7)	0.0039 (7)
C6	0.0133 (9)	0.0129 (8)	0.0125 (9)	0.0028 (7)	0.0048 (7)	0.0039 (7)
C7	0.0157 (10)	0.0173 (9)	0.0114 (8)	0.0058 (7)	0.0039 (7)	0.0065 (7)
C8	0.0193 (11)	0.0212 (11)	0.0342 (12)	0.0067 (8)	0.0092 (9)	−0.0032 (9)
C9	0.0153 (10)	0.0160 (8)	0.0149 (9)	0.0054 (7)	0.0059 (7)	0.0075 (7)
C10	0.0185 (10)	0.0228 (10)	0.0153 (9)	0.0030 (8)	0.0048 (8)	0.0071 (8)
C11	0.0245 (11)	0.0256 (10)	0.0137 (9)	0.0051 (9)	0.0059 (8)	0.0071 (8)
C12	0.0226 (11)	0.0253 (10)	0.0147 (9)	0.0066 (8)	0.0083 (8)	0.0088 (8)
C13	0.0136 (10)	0.0125 (8)	0.0137 (8)	0.0024 (7)	0.0019 (7)	0.0033 (7)
C14	0.0189 (11)	0.0157 (9)	0.0179 (9)	0.0036 (8)	0.0040 (8)	0.0078 (8)
C15	0.0211 (11)	0.0135 (9)	0.0223 (10)	0.0032 (8)	0.0002 (8)	0.0067 (8)
C16	0.0182 (10)	0.0152 (9)	0.0204 (9)	0.0068 (7)	0.0016 (8)	0.0019 (7)
C17	0.0167 (10)	0.0201 (9)	0.0173 (9)	0.0064 (8)	0.0054 (7)	0.0046 (8)
C18	0.0166 (10)	0.0119 (8)	0.0129 (8)	0.0061 (7)	0.0048 (7)	0.0049 (7)
C19	0.0245 (11)	0.0264 (10)	0.0127 (9)	0.0052 (9)	0.0070 (8)	0.0023 (8)
N1	0.0166 (9)	0.0159 (8)	0.0165 (8)	0.0055 (6)	0.0050 (6)	0.0057 (6)
O1	0.0222 (8)	0.0200 (7)	0.0170 (6)	0.0095 (6)	0.0071 (6)	0.0107 (5)
O2	0.0192 (8)	0.0158 (7)	0.0218 (7)	0.0010 (6)	0.0061 (6)	0.0045 (5)
O3	0.0150 (7)	0.0166 (7)	0.0222 (7)	0.0055 (5)	0.0065 (6)	0.0023 (6)
O4	0.0219 (8)	0.0150 (6)	0.0170 (6)	0.0035 (6)	0.0083 (6)	0.0059 (5)
O5	0.0183 (7)	0.0181 (7)	0.0128 (6)	0.0020 (5)	0.0049 (5)	0.0039 (5)
S1	0.0179 (2)	0.0223 (2)	0.0148 (2)	−0.00028 (18)	0.00576 (16)	0.00623 (17)

Geometric parameters (Å, º) top

C1—O1	1.215 (2)	C10—C11	1.426 (3)
C1—C6	1.484 (3)	C10—H10	0.9500
C1—C2	1.526 (2)	C11—C12	1.353 (3)
C2—C7	1.515 (3)	C11—H11	0.9500
C2—C3	1.546 (3)	C12—S1	1.725 (2)
C2—H2	1.0000	C12—H12	0.9500
C3—C9	1.499 (2)	C13—N1	1.349 (2)
C3—C4	1.529 (2)	C13—C14	1.400 (3)
C3—H3	1.0000	C14—C15	1.384 (3)
C4—C5	1.509 (3)	C14—H14	0.9500
C4—H4A	0.9900	C15—C16	1.386 (3)
C4—H4B	0.9900	C15—H15	0.9500
C5—C6	1.353 (3)	C16—C17	1.391 (3)
C5—C13	1.485 (3)	C16—H16	0.9500
C6—C18	1.508 (2)	C17—N1	1.335 (3)
C7—O2	1.207 (2)	C17—H17	0.9500
C7—O3	1.335 (2)	C18—O4	1.199 (2)
C8—O3	1.452 (2)	C18—O5	1.344 (2)
C8—H8A	0.9800	C19—O5	1.448 (2)
C8—H8B	0.9800	C19—H19A	0.9800
C8—H8C	0.9800	C19—H19B	0.9800
C9—C10	1.364 (3)	C19—H19C	0.9800
C9—S1	1.733 (2)

O1—C1—C6	121.66 (16)	C3—C9—S1	123.13 (14)
O1—C1—C2	121.05 (17)	C9—C10—C11	113.26 (19)
C6—C1—C2	117.28 (15)	C9—C10—H10	123.4
C7—C2—C1	111.28 (15)	C11—C10—H10	123.4
C7—C2—C3	108.90 (15)	C12—C11—C10	112.96 (18)
C1—C2—C3	109.64 (15)	C12—C11—H11	123.5
C7—C2—H2	109.0	C10—C11—H11	123.5
C1—C2—H2	109.0	C11—C12—S1	111.23 (15)
C3—C2—H2	109.0	C11—C12—H12	124.4
C9—C3—C4	113.33 (15)	S1—C12—H12	124.4
C9—C3—C2	113.64 (16)	N1—C13—C14	122.33 (18)
C4—C3—C2	108.56 (15)	N1—C13—C5	116.34 (17)
C9—C3—H3	107.0	C14—C13—C5	121.32 (17)
C4—C3—H3	107.0	C15—C14—C13	118.75 (18)
C2—C3—H3	107.0	C15—C14—H14	120.6
C5—C4—C3	110.93 (15)	C13—C14—H14	120.6
C5—C4—H4A	109.5	C14—C15—C16	119.19 (19)
C3—C4—H4A	109.5	C14—C15—H15	120.4
C5—C4—H4B	109.5	C16—C15—H15	120.4
C3—C4—H4B	109.5	C15—C16—C17	118.38 (19)
H4A—C4—H4B	108.0	C15—C16—H16	120.8
C6—C5—C13	122.14 (17)	C17—C16—H16	120.8
C6—C5—C4	120.52 (17)	N1—C17—C16	123.48 (19)
C13—C5—C4	117.32 (16)	N1—C17—H17	118.3
C5—C6—C1	122.52 (16)	C16—C17—H17	118.3
C5—C6—C18	123.87 (17)	O4—C18—O5	125.11 (17)
C1—C6—C18	113.58 (15)	O4—C18—C6	123.28 (18)
O2—C7—O3	123.86 (18)	O5—C18—C6	111.52 (16)
O2—C7—C2	124.32 (18)	O5—C19—H19A	109.5
O3—C7—C2	111.70 (16)	O5—C19—H19B	109.5
O3—C8—H8A	109.5	H19A—C19—H19B	109.5
O3—C8—H8B	109.5	O5—C19—H19C	109.5
H8A—C8—H8B	109.5	H19A—C19—H19C	109.5
O3—C8—H8C	109.5	H19B—C19—H19C	109.5
H8A—C8—H8C	109.5	C17—N1—C13	117.88 (17)
H8B—C8—H8C	109.5	C7—O3—C8	114.76 (16)
C10—C9—C3	126.53 (18)	C18—O5—C19	113.04 (15)
C10—C9—S1	110.34 (15)	C12—S1—C9	92.21 (10)

O1—C1—C2—C7	29.2 (3)	C3—C9—C10—C11	179.62 (19)
C6—C1—C2—C7	−151.60 (17)	S1—C9—C10—C11	−0.2 (2)
O1—C1—C2—C3	149.70 (18)	C9—C10—C11—C12	0.2 (3)
C6—C1—C2—C3	−31.1 (2)	C10—C11—C12—S1	−0.2 (2)
C7—C2—C3—C9	−51.8 (2)	C6—C5—C13—N1	−20.6 (3)
C1—C2—C3—C9	−173.75 (15)	C4—C5—C13—N1	157.70 (17)
C7—C2—C3—C4	−178.86 (15)	C6—C5—C13—C14	160.74 (19)
C1—C2—C3—C4	59.17 (19)	C4—C5—C13—C14	−20.9 (3)
C9—C3—C4—C5	174.49 (16)	N1—C13—C14—C15	0.4 (3)
C2—C3—C4—C5	−58.3 (2)	C5—C13—C14—C15	178.96 (17)
C3—C4—C5—C6	28.6 (3)	C13—C14—C15—C16	−0.3 (3)
C3—C4—C5—C13	−149.71 (17)	C14—C15—C16—C17	0.5 (3)
C13—C5—C6—C1	179.18 (17)	C15—C16—C17—N1	−0.9 (3)
C4—C5—C6—C1	0.9 (3)	C5—C6—C18—O4	107.7 (2)
C13—C5—C6—C18	1.4 (3)	C1—C6—C18—O4	−70.2 (2)
C4—C5—C6—C18	−176.85 (18)	C5—C6—C18—O5	−75.7 (2)
O1—C1—C6—C5	179.91 (19)	C1—C6—C18—O5	106.35 (19)
C2—C1—C6—C5	0.7 (3)	C16—C17—N1—C13	0.9 (3)
O1—C1—C6—C18	−2.1 (3)	C14—C13—N1—C17	−0.7 (3)
C2—C1—C6—C18	178.65 (16)	C5—C13—N1—C17	−179.31 (17)
C1—C2—C7—O2	50.6 (3)	O2—C7—O3—C8	6.2 (3)
C3—C2—C7—O2	−70.3 (2)	C2—C7—O3—C8	−169.87 (18)
C1—C2—C7—O3	−133.27 (17)	O4—C18—O5—C19	−8.5 (3)
C3—C2—C7—O3	105.76 (18)	C6—C18—O5—C19	174.97 (15)
C4—C3—C9—C10	−122.9 (2)	C11—C12—S1—C9	0.08 (18)
C2—C3—C9—C10	112.5 (2)	C10—C9—S1—C12	0.06 (16)
C4—C3—C9—S1	56.8 (2)	C3—C9—S1—C12	−179.74 (17)
C2—C3—C9—S1	−67.7 (2)

Hydrogen-bond geometry (Å, º) top

Cg1 and Cg2 are the centroids of the S1/C9–C12 thiophene and N1/C13–C17 pyridine rings, respectively.

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···O3ⁱ	1.00	2.64	3.625 (2)	168
C8—H8C···O2ⁱⁱ	0.98	2.35	3.215 (3)	146
C11—H11···O1ⁱⁱⁱ	0.95	2.62	3.193 (2)	119
C12—H12···O4^iv	0.95	2.50	3.446 (2)	180
C14—H14···O2^v	0.95	2.61	3.468 (2)	151
C16—H16···O1^vi	0.95	2.52	3.305 (3)	140
C19—H19B···O2^vii	0.98	2.64	3.584 (3)	161
C4—H4A···Cg2ⁱⁱ	0.99	2.94	3.841 (2)	152
C19—H19C···Cg1^viii	0.98	2.78	3.659 (3)	149

Symmetry codes: (i) x−1, y, z; (ii) x+1, y, z; (iii) x, y, z−1; (iv) x+1, y, z−1; (v) x, y+1, z; (vi) x−1, y+1, z; (vii) x, y+1, z+1; (viii) x, y, z+1.

Acknowledgements

Authors' contributions are as follows. Conceptualization, IGM, ANK and FNN; methodology, IGM and MA; investigation, VNK and FNN; writing (original draft), MA, AB and ANK, writing (review and editing of the manuscript), İGM and ANK; visualization, MA, EZH and FNN; funding acquisition, VNK, AB and FNN; resources, AB, VNK and MA; supervision, MA and ANK.

Funding information

This paper was supported by Baku State University and the RUDN University Strategic Academic Leadership Program.

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